/**
 * \file  sequence.h
 * \brief Definition of SequenceSet and Resistance Type.
 *
 * LAV: Lib Anti Virals
 * <http://aso.googlecode.com/>
 * Copyright (C) 2010 Velez Ezequiel, Peralta Andres, FuDePAN
 *
 * This file is part of the LAV project.
 *
 * Contents:       Header file for LAV providing type SequenceSet and Resistance.
 *
 * System:         LAV
 * Language:       C++
 *
 * Author:         Velez Ezequiel, Peralta Andres
 * E-Mail:
 *
 * LAV is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * LAV is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with LAV.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifndef SEQUENCE_H
#define SEQUENCE_H

#include <biopp/biopp.h>
#include "lav/aso_exception.h"
#include <mili/mili.h>


namespace lav
{

/**
 * This typedef represents the set of aminoacids sequence redefinition to sequence set
 *
 */
typedef std::list<biopp::PseudoNucSequence> SequenceSet;


/**
 * This method loads a nucleotids sequence from a file
 *
 *@Param seq_file Represents the file's path where the information is allocated
 *@Param sequence The file information will be load here
 *
 */
void load_sequence(const char* seq_file, biopp::PseudoNucSequence& sequence);


/**
 * This method prints the aminoacids (nucleotids) sequence
 *
 *@Param sequence Represents the information which will be print
 *
 */
void print_sequence(const biopp::PseudoNucSequence& sequence);


}

#endif

